Protein Interaction Mapping related to Becker Muscular Dystrophy.

Objective
Becker Muscular Dystrophy (BMD) is a neuromuscular disorder which is incurable. In this research protein interaction network of most associated proteins with BMD to provide better clarification of disorder underlying mechanism was investigated.


Materials & Methods
The related genes to BMD were retrieved via string database and conducted by Cytoscape and the related algorithms. The network centrality analysis was performed based on degree, betweenness, closeness, and stress parameters. Gene ontology and clustering were performed via ClueGO analysis.


Results
DMD as the super-hub as well as other central proteins including UTRN, TTN, DNM2, and RYR1 are important in BMD in terms of interactive features. The impairment of muscular contraction may be vital in BMD disease pathogenesis as it is the highlighted biological process term obtained by ClueGO analysis.


Conclusion
DMD targeting may be the main concern for dystrophy clinical approaches. However, the other suggested proteins should be evaluated. Targeting these key proteins are required for treatment goals following extensive validation studies.


Introduction
Becker Muscular Dystrophy is a less severe type of dystrophy than Duchenne muscular dystrophy (1). This type of neuromuscular disorder is mainly known with dysfunctional protein dystrophin (2).
As there is no therapy available for BMD, molecular examination can be helpful in this regard (3).
The potential molecules contributing to disease pathogenesis can be targeted for treatments (4,5). Many investigations in this light have been conducted and provided further information about this disease and with possible usage in clinical goals (6). The analysis conducted up until today showed the contribution of many molecules for this disease that worth more evaluations (7,8).
However, due to the complex molecular nature of muscular dystrophy, more studies in terms of proteins as the functional level of cell is required (9).
The way these proteins communicate can their linkage results in many different phenotypes are known as protein-protein interaction network (10). Any changes in this interaction unit may lead to phenotype alterations and sometimes the manifestation of a specific disease. This procedure is related to how the communication of these proteins can affect other proteins and the contributing pathways (11). Therefore, by analyzing these features the possible knowledge of molecular behavior of any kinds of diseases can be better understood (12). In addition, by examining proteins with prioritized topological features, potential nominates for biomarker discovery can be introduced.
Moreover, more in-depth knowledge can be achieved through these studies by exploring the functional roles and biological processes related to these central proteins (13). On the other hand, expression changes in these types may result in vast dysregulation in the whole PPI network and accordingly, a disease phenotype may manifest (13). Etiology of Becker muscular dystrophy can be better explained by protein-protein interaction (PPI) network analysis and wide validation methods applications. Here, an introductory network value of this important muscular disease is suggested.

Materials & Methods
For the network construction, the used application was Cytoscape 3.4.0. (14). Through Cytoscape, STRING Database provided the essential information for interaction pattern by the use of different sources and combined confidence score Cytoscape plug-ins explored the gene ontology (GO) annotations (18,19). Controlled vocabulary of three biological annotations including cellular component, molecular function, and biological process terms are implemented by GO source (20).
The statistical test for this analysis was Kappa score.
High kappa score indicates the higher possibility that terms group together. The cut off for here was set 0.5. In addition, genes per term was considered 3 and the percentage was set to 4. The minimum and maximum level of ontology were set to 3 to 8 as the default option, respectively. The P-value was also set to ≤0.05 and Bonferroni step down as the correction method. Two-sided (enrichment/ depletion) based on hypergeometric test was also selected as the default option.

Results
Protein network construction of Becker muscular dystrophy via String Database and Cytoscape is shown in Figure 1.   (Table 1). If a protein was hub or bottleneck and was included in the selected nodes based on closeness and stress was introduced as as a crucial protein proteins (Table 2). Gene ontology examination can be handled by the application of ClueGO. Here, the biological process evaluation of the main network was assessed (Figure 2).  The network statistical properties are as follow: P<0.05, Kappa Score=0.5.

Discussion
Topological examination implements remarkable properties of interaction basis of molecular concept of any kinds of diseases (21). Proteins with such characteristics are essential for network integrity and strength (22). In this study, proteins with such properties are suggested for BMD. In Figure 1, the first component of the network is a medium network that the most essential properties are contributing in this part. Other components are isolated or small communities not considered. No interactions between these nodes and the main network may be due to either undiscovered interactions or insignificant contribution of these proteins for BMD. The range of contribution of the isolated nodes to the disease is between 0.5-1 and for the other nodes is between 0.5-4 ( Table 2).

Discussion
Topological examination implements remarkable properties of interaction basis of molecular concept of any kinds of diseases (21). Proteins with such characteristics are essential for network integrity and strength (22). In this study, proteins with such properties are suggested for BMD. In In conclusion, DMD targeting may be the main concern for dystrophy clinical approaches.